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1.ABSTRACTOrganoids arein vitromodel systems generated from tissues. Organoids express specific physiological functions associated with their original tissue location and they express tissue-segment-specific genes. The aim of this study was to culture pig organoids from different areas of intestinal segments: duodenum, ileum (with or without Peyers Patches (PP)), and colon, to investigate the resemblance with thein vivotissues and variability of multiple adjacent sampling sites based on histology and transcriptome profiles. The transcriptome profiles of thein vivotissues and the derived organoids showed high resemblance for all intestinal segments. For the transcriptomic cluster analysis it was shown that it is important to use tissue important genes to shown the resemble between tissue and their derived organoids. The transcriptome profiles clearly separated the intestinal segments, and samples of the same segment from adjacent tissue locations showed high transcriptome profile similarity. Ileum samples with and without PP were also separated. Pathway analysis of differentially expressed genes from PP compared with non-PP suggested the importance of several aspects of cell cycle progression regulation, including DNA metabolism, chromatin organization, regulation of mitotic stage progression, and regulation of inflammation. Based primarily on the transcriptomics results, we conclude that organoids reflect the sampled intestinal segment and that organoids derived from adjacent sampling sites in an intestinal tissue segment showed low variability. The results from the ileum indicate that organoids have potential to study intestinal innate immune processes.

Organoids are self-organizing, self-renewing three-dimensional cellular structures that resemble organs in structure and function. They can be derived from adult stem cells, embryonic stem cells, or induced pluripotent stem cells. They contain most of the relevant cell types with a topology and cell-to-cell interactions resembling that of the in vivo tissue. The widespread and increasing adoption of organoid-based technologies in human biomedical research is testament to their enormous potential in basic, translational- and applied-research. In a similar fashion there appear to be ample possibilities for research applications of organoids from livestock and companion animals. Furthermore, organoids as in vitro models offer a great possibility to reduce the use of experimental animals. Here, we provide an overview of studies on organoids in livestock and companion animal species, with focus on the methods developed for organoids from a variety of tissues/organs from various animal species and on the applications in veterinary research. Current limitations, and ongoing research to address these limitations, are discussed. Further, we elaborate on a number of fields of research in animal nutrition, host-microbe interactions, animal breeding and genomics, and animal biotechnology, in which organoids may have great potential as an in vitro research tool.

Mortality due to feather pecking (FP) has large economic and welfare consequences in the commercial poultry industry, and reduces survival of birds. With FP, the survival time of a hen depends both on her own genetic ability to avoid becoming the victim of FP (direct genetic effect; DGE), and on the genetic tendency of her group mates to perform FP (indirect genetic effect; IGE). Thus, to improve survival time of laying hens, it is important to use a breeding strategy that captures both the DGE and the IGE of selection candidates. Here, we investigate the prospects for solving mortality due to FP in laying hens by genetic selection. First, we review genetic parameters for survival time. Second, we use deterministic simulation to predict response to selection for 2 multi-trait crossbred breeding programs, a traditional recurrent testing scheme (RT) and a genomic selection scheme (GS). Finally, we investigate the prospects for sustained improvement of survival time when mortality becomes low. Results show that survival time has considerable heritable variation; most estimates of the total additive genetic standard deviation are larger than 1 mo. As expected, predicted single generation response to selection in survival time with GS is substantial larger than with RT. Particularly when the correlation between survival time and other breeding goal traits is zero, the GS scheme yields substantial improvement in survival time. For example, when mortality is 35%, the genetic correlation between survival time and other traits is 0, allowing for a 10% reduction of response in other traits, and when selection takes place in both the sire line and dam line, survival time can be improved with ∼23 D in one generation, using GS. Results, however, also show a strong decrease in heritability when mortality decreases, indicating that continued improvement becomes increasingly difficult. In summary, our results show that breeders can considerably reduce mortality due to FP with limited reduction of improvement in other breeding goal traits.

Mortality of laying hens due to cannibalism is a major problem in the egg-laying industry. Survival depends on two genetic effects: the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its group mates (IGE). For hens housed in sire-family groups, DGE and IGE cannot be estimated using pedigree information, but the combined effect of DGE and IGE is estimated in the total breeding value (TBV). Genomic information provides information on actual genetic relationships between individuals and might be a tool to improve TBV accuracy. We investigated whether genomic information of the sire increased TBV accuracy compared with pedigree information, and we estimated genetic parameters for survival time. A sire model with pedigree information (BLUP) and a sire model with genomic information (ssGBLUP) were used. We used survival time records of 7290 crossbred offspring with intact beaks from four crosses. Cross-validation was used to compare the models. Using ssGBLUP did not improve TBV accuracy compared with BLUP which is probably due to the limited number of sires available per cross (~50). Genetic parameter estimates were similar for BLUP and ssGBLUP. For both BLUP and ssGBLUP, total heritable variance (T2 ), expressed as a proportion of phenotypic variance, ranged from 0.03 ± 0.04 to 0.25 ± 0.09. Further research is needed on breeding value estimation for socially affected traits measured on individuals kept in single-family groups.

Simple Summary The European Cooperation in Science and Technology (COST) Action GroupHouseNet aims to provide synergy among scientists to prevent damaging behavior in group-housed pigs and laying hens. One goal of this network is to determine how genetic and genomic tools can be used to breed animals that are less likely to perform damaging behavior on their pen-mates. In this review, the focus is on feather-pecking behavior in laying hens. Reducing feather pecking in large groups of hens is a challenge, because it is difficult to identify and monitor individual birds. However, current developments in sensor technologies and animal breeding have the potential to identify individual animals, monitor individual behavior, and link this information back to the underlying genotype. We describe a combination of sensor technologies and “-omics” approaches that could be used to select against feather-pecking behavior in laying hens. Abstract Damaging behaviors, like feather pecking (FP), have large economic and welfare consequences in the commercial laying hen industry. Selective breeding can be used to obtain animals that are less likely to perform damaging behavior on their pen-mates. However, with the growing tendency to keep birds in large groups, identifying specific birds that are performing or receiving FP is difficult. With current developments in sensor technologies, it may now be possible to identify laying hens in large groups that show less FP behavior and select them for breeding. We propose using a combination of sensor technology and genomic methods to identify feather peckers and victims in groups. In this review, we will describe the use of “-omics” approaches to understand FP and give an overview of sensor technologies that can be used for animal monitoring, such as ultra-wideband, radio frequency identification, and computer vision. We will then discuss the identification of indicator traits from both sensor technologies and genomics approaches that can be used to select animals for breeding against damaging behavior.

Survival of commercial laying hens is an important trait. Feather pecking has a large effect on the survival of birds. To improve survival it is important to use quantitative genetic methods that take into account both the direct genetic effect (victim effect) and the indirect genetic effect (actor effect). For survival time, we found that the victim effect contributes 13-64% of total heritable variation, while the actor effect contributes 36-87% of total heritable variation. Together, they explain 15-26% of total phenotypic variation in survival time. Here we compare different breeding programme designs to identify the optimum selection strategy against mortality due to feather pecking. Results show that mortality due to feather pecking can be reduced using genetic approaches, taking into account direct and indirect genetic effects. We performed a selection experiment using selection based on relatives. Using this method enables selection against mortality due to feather pecking in laying hens. However, selection intensities were small. Genomic selection can be a promising tool to select against mortality due to feather pecking. Model predictions show that genomic selection is expected to yield a rapid reduction of mortality due to feather pecking, but a challenge will be to reduce mortality due to feather pecking in large groups.

Individual data on activity of broilers is valuable, as activity may serve as a proxy for multiple health, welfare and performance indicators. However, broilers are often kept in large groups, which makes it difficult to identify and monitor them individually. Sensor technologies might offer solutions. Here, an ultra-wideband (UWB) tracking system was implemented with the goal of validating this system for individual tracking of activity of group-housed broilers. The implemented approaches were (1) a comparison of distances moved as recorded by the UWB system and on video and (2) a study recording individual levels of activity of broilers and assessing group-level trends in activity over time, that could be compared to activity trends from literature. There was a moderately strong positive correlation between the UWB system and video tracking. Using the UWB system, we detected reductions in activity over time and we found that lightweight birds were on average more active than heavier birds. Both findings match with reports in literature. Overall, the UWB system appears well-suited for activity monitoring in broilers, when the settings are kept the same for all individuals. The longitudinal information on differences in activity can potentially be used as proxy for health, welfare and performance, but further research into individual patterns in activity is required.

Indirect genetic effects (IGEs) are the basis of social interactions among conspecifics, and can affect genetic variation of nonsocial and social traits. We used flour beetles (Tribolium castaneum) of two phenotypically distinguishable populations to estimate genetic (co)variances and the effect of IGEs on three life-history traits: development time (DT), growth rate (GR), and pupal body mass (BM). We found that GR was strongly affected by social environment with IGEs accounting for 18% of the heritable variation. We also discovered a sex-specific social effect: male ratio in a group significantly affected both GR and BM; that is, beetles grew larger and faster in male-biased social environments. Such sex-specific IGEs have not previously been demonstrated in a nonsocial insect. Our results show that beetles that achieve a higher BM do so via a slower GR in response to social environment. Existing models of evolution in age-structured or stage-structured populations do not account for IGEs of social cohorts. It is likely that such IGEs have played a key role in the evolution of developmental plasticity shown by Tenebrionid larvae in response to density. Our results document an important source of genetic variation for GR, often overlooked in life-history theory.

Feather pecking (FP) in laying hens may cause mortality due to cannibalism. Novel breeding methods using survival days of group-housed siblings allow for the genetic selection of laying hens with low mortality (LML: low mortality line) due to cannibalism. Previous studies have demonstrated less fear-related behavior and also less FP in LML hens compared to CL. Selection also caused changes in locomotor behavior in an open field. It is unknown, however, whether selection for low mortality affects central neurotransmitter levels. In this study, brain monoamine levels were measured in the dorsal thalamus, medial striatum, hippocampus and arcopallium of adult laying hens of both LML and CL using HPLC. Brain samples were collected after 5-min of manual restraint. The most prominent line differences were found in the arcopallium. Compared to CL, LML had lower levels of noradrenaline (NA) and 3,4-dihydroxyphenylacetic acid (DOPAC) and tended to have lower levels of dopamine (DA), homovanillic acid (HVA), and 5-hydroxyindoleacetic acid (5-HIAA). Levels of serotonin (5-HT), 5-HT- and DA-turnover in this brain area were not affected by line. LML showed less fear-related behavior during the restraint than CL. These findings show that selection for low mortality in hens leads to changes of predominantly the dopaminergic system in the chicken's arcopallium, a forebrain somatomotor area also related to fear. This suggests a relationship between catecholamine functioning in this brain area and FP and cannibalistic behavior in chickens and underpins previously found relationships between FP, fear and high activity.

article i nfo Severe feather pecking (SFP) in laying hens is a detrimental behavior causing loss of feathers, skin damage and cannibalism. Previously, we have associated changes in frontal brain serotonin (5-HT) turnover and dopamine (DA) turnover with alterations in feather pecking behavior in young pullets (28-60 days). Here, brain monoaminelevelsweremeasuredinadultlayinghens;focusingonfourbrainareasthatareinvolvedinemotion- al behavior or are part of the basal ganglia-thalamopallial circuit, which is involved in obsessive compulsive disorders. Three behavioral phenotypes were studied: Severe Feather Peckers (SFPs), Victims of SFP, and Non- Peckers (NPs). Hens (33 weeks old) were sacrificed after a 5-min manual restraint test. SFPs had higher 5- HIAA levels and a higher serotonin turnover (5-HIAA/5-HT) in the dorsal thalamus than NPs, with intermediate levels in victims. NPs had higher 5-HT levels in the medial striatum than victims, with levels of SFPs in between. 5-HT turnover levels did not differ between phenotypes in medial striatum, arcopallium and hippocampus. DA turnover levels were not affected by feather pecking phenotype. These findings indicate that serotonergic neurotransmission in the dorsal thalamus and striatum of adult laying hens depends on differences in behavioral feather pecking phenotype, with, compared to non-pecking hens, changes in both SFP and their victims. Further identification of different SFP phenotypes is needed to elucidate the role of brain monoamines in SFP.

Fearfulness of an individual can affect its sensitivity to stress, while at the same time the social situation in which an animal lives can affect its fear level. It is however unknown what the long-term effects of high fearfulness on sensitivity to stress are, on individual or group level in laying hens. We hypothesize that increased fearfulness at a young age results in increased sensitivity to stress at an adult age, and that this relation can differ between groups, due to differences in group composition. Therefore, we studied the relation between fearfulness in an Open Field (OF) test at six weeks of age and plasma-corticosterone (CORT) levels after a 5-min Manual Restraint test (MR) at 33 weeks of age, and assessed behavior in the home pen. We used birds from a low mortality line, selected for four generations on low mortality due to feather pecking and cannibalism and a control line (n=153 in total, eight pens/line). These lines are known to differ in fearfulness and stress physiology. Chicks from the low mortality line were more active in the OF compared to chicks from the control line. Chicks that showed a fearful response (no walking, no vocalizing) in the OF test had higher CORT at 33 weeks of age than chicks that walked and/or vocalized in the OF test and had higher activity in the home pen as adults. On group level, a passive response in the OF was related to high CORT levels after MR. Presence of at least one fearful bird in a group led to higher CORT in the other group mates compared to birds from groups with no fearful birds present. Birds from groups in which more than 50% of birds had severe comb lesions had higher CORT levels compared to birds from groups with less than 50% of birds affected. High fearfulness of laying hen chicks can on individual level have a long-term effect on stress sensitivity. The presence of fearful birds in a group as well as signs of social instability in a group, indicated by comb lesions, can affect sensitivity to stress of birds from the same group. The mechanism by which this occurs can lie in social transmission of (fear related) behavior, but this suggestion needs further investigation. (C) 2012 Elsevier Inc. All rights reserved.

Feather pecking and cannibalism in chickens can lead to injury or to death of the vic- tims, and is thus a serious welfare and economic issue in modern poultry farming. A sib selection scheme has been initiated to genetically select a low mortality line (LML), which shows decreased mortality due to cannibalism compared to a control line (CL). To determine whether undesired behavioural effects such as impaired cognition, increased fearfulness, or increased anxiety might have inadvertently been co-selected, we tested hens from the fourth generation of selection (n = 9 per selection line) in several behavioural tasks. When tested in a 122 cm × 122 cm open field at age 7 days, the lines showed no differences in locomotion or vocalization. In a T-maze test in which the chickens could navigate to find conspecifics, testing sociality and fearfulness, 12 to 16-day-old CL chickens showed a lack of exploratory behaviour; they did not leave the start box. In contrast, most LML chickens negotiated the maze, and approximately half of them found and stayed close to their con- specifics. This difference points toward higher levels of fearfulness in the CL than LML. In a voluntary approach test assessing fearfulness for humans, conducted when the chicks were 26 days old, the LML approached a familiar human faster, thus displaying lower levels of fearfulness. The same birds were tested in a holeboard test at an age of 25-65 days, the first time this test of spatial memory has been used in an avian species. Our results demonstrated high levels of working memory performance and low levels of reference memory perfor- mance in both lines, with no differences between the lines. Overall, the present results indicate that unwanted behavioural effects were not co-selected with selection on low mortality, and support the feasibility of the use of the LML in farming practice. © 2011 Elsevier B.V. All rights reserved.

Social interactions, especially those involving competition among individuals, are important in domesticated livestock and in natural populations. The heritability of traits affected by such interactions has two components, one originating in the individual like that of classical traits (direct effects) and the other originating in other group members (indirect effects). The latter type of trait represents a significant source of ‘hidden heritability’ and it requires population structure and knowledge from relatives in order to access it for selective breeding. When ignored, competitive interactions may increase as an indirect response to direct selection, resulting in diminished yields. We illustrate how population genetic structure affects the response to selection of traits with indirect genetic effects using population genetic and quantitative genetic theory. Population genetic theory permits us to connect our results to the existing body of theory on kin and group selection in natural populations. The quantitative genetic perspective allows us to see how breeders have used knowledge from relatives and family selection in the domestication of plants and animals to improve the welfare and production of livestock by incorporating social genetic effects in the breeding program. We illustrate the central features of these models by reviewing empirical studies from domesticated chickens.

Under commercial conditions, data on egg production in laying hens are usually collected per cage rather than individually. In current breeding programs, genetic evaluations are, however, based on individually recorded egg production. Because commercial flocks are not maintained in single cages, this environmental difference between the breeding and commercial setting may result in a genotype x environment interaction. This study was aimed at estimating genetic parameters and predicting estimated breeding values for early egg production of laying hens by using pooled data (i.e., data from multiple bird cages) from pedigree birds housed in 4-bird cages. Using cage records, we compared 2 different methods of handling pooled data: cage sums and the assignment of cage means to individual birds, referred to as the approximate method. The 2 methods were compared by using cross-validation. Data from 3 purebred White Leghorn layer lines were used. Estimated heritability for early egg production was 0.36 when cage sums were used and 0.30 with the approximate method. The correlation of estimated breeding values between the cage sums method and the approximate method was 0.88. Cross-validation showed that the use of cage sums led to better predictions of missing phenotypes compared with the approximate method. The results of the research demonstrate that pooled data can be used in the genetic evaluation of laying hens and show that using directly pooled records (e.g., cage sums) gives better results than assigning group means to the birds of the group, thus simulating individual records.

Mortality due to cannibalism is a major problem in laying hens. Due to prohibition of beak-trimming in the European Union, this problem will increase in the near future. One solution to reduce mortality due to cannibalism is to use genetic selection. Mortality due to cannibalism, however, differs from conventional breeding traits, because it depends on social interactions among individuals. Selection strategies aiming to reduce cannibalism, therefore, should consider both the direct effect of an individual on its own survival and the social effect of the individual on the survival of its group members (the so-called associative effect). Traditional breeding, however, accounts for only the direct effect. Recently, methods have been proposed to estimate variance components and breeding values for both direct and associative effects. This paper presents estimated genetic parameters for direct and associative effects on survival days in 3 purebred laying lines. For the analysis, 16,780 hens with intact beaks were used. When considering only direct effects, heritabilities ranged from 2 through 10%. When considering both direct and associative effects, the total heritable variance, expressed as a proportion of phenotypic variance, ranged from 6 through 19%. These results show that heritable variation in survival days is substantially larger than suggested by conventional direct effects models. This means that prospects for reducing mortality by means of genetic selection are good and may lead to substantial reduction of 1 of the major welfare problems in egg production.

The combination of breeding for increased production and the intensification of housing conditions have resulted in increased occurrence of behavioral, physiological, and immunological disorders. These disorders affect health and welfare of production animals negatively. For future livestock systems, it is important to consider how to manage and breed production animals. In this paper, we will focus on selective breeding of laying hens. Selective breeding should not only be defined in terms of production, but should also include traits related to animal health and welfare. For this we like to introduce the concept of robustness. The concept of robustness includes individual traits of an animal that are relevant for health and welfare. Improving robustness by selective breeding will increase (or restore) the ability of animals to interact successfully with the environment and thereby to make them more able to adapt to an appropriate husbandry system. Application of robustness into a breeding goal will result in animals with improved health and welfare without affecting their integrity. Therefore, in order to be ethically acceptable, selective breeding in animal production should accept robustness as a breeding goal.

Indirect genetic effects (IGEs) are the basis of social interactions among conspecifics, and can affect genetic variation of nonsocial and social traits. We used flour beetles (Tribolium castaneum) of two phenotypically distinguishable populations to estimate genetic (co)variances and the effect of IGEs on three life-history traits: development time (DT), growth rate (GR), and pupal body mass (BM). We found that GR was strongly affected by social environment with IGEs accounting for 18% of the heritable variation. We also discovered a sex-specific social effect: male ratio in a group significantly affected both GR and BM; that is, beetles grew larger and faster in male-biased social environments. Such sex-specific IGEs have not previously been demonstrated in a nonsocial insect. Our results show that beetles that achieve a higher BM do so via a slower GR in response to social environment. Existing models of evolution in age-structured or stage-structured populations do not account for IGEs of social cohorts. It is likely that such IGEs have played a key role in the evolution of developmental plasticity shown by Tenebrionid larvae in response to density. Our results document an important source of genetic variation for GR, often overlooked in life-history theory.

Background Minimizing bird losses is important in the commercial layer industry. Selection against mortality is challenging because heritability is low, censoring is high, and individual survival depends on social interactions among cage members. With cannibalism, mortality depends not only on an individual’s own genes (direct genetic effects; DGE) but also on genes of its cage mates (indirect genetic effects; IGE). To date, studies using DGE–IGE models have focussed on survival time but their shortcomings are that censored records were considered as exact lengths of life and models assumed that IGE were continuously expressed by all cage members even after death. However, since dead animals no longer express IGE, IGE should ideally be time-dependent in the model. Neglecting censoring and timing of IGE expression may reduce accuracy of estimated breeding values (EBV). Thus, our aim was to improve prediction of breeding values for survival time in layers that present cannibalism. Methods We considered four DGE–IGE models to predict survival time in layers. One model was an analysis of survival time and the three others treated survival in consecutive months as a repeated binomial trait (repeated measures models). We also tested whether EBV were improved by including timing of IGE expression in the analyses. Approximate EBV accuracies were calculated by cross-validation. The models were fitted to survival data on two purebred White Leghorn layer lines W1 and WB, each having monthly survival records over 13 months. Results Including the timing of IGE expression in the DGE–IGE model reduced EBV accuracy compared to analysing survival time. EBV accuracy was higher when repeated measures models were used. However, there was no universal best model. Using repeated measures instead of analysing survival time increased EBV accuracy by 10 to 21 and 2 to 12 % for W1 and WB, respectively. We showed how EBV and variance components estimated with repeated measures models can be translated into survival time. Conclusions Our results suggest that prediction of breeding values for survival time in laying hens can be improved using repeated measures models. This is an important result since more accurate EBV contribute to higher rates of genetic gain. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0152-2) contains supplementary material, which is available to authorized users.

In a commentary in Frontiers, Van Rooijen (2014) states: “Today the developments in genetics are exciting. Perhaps this explains why geneticists sometimes seem to overlook common sense solutions. One example of this is the selection experiment done by Bijma et al. (2007a,b). ……As a result their selection seemed not very efficient.” In those two papers, however, we do not report a selection experiment. The first paper presents general quantitative genetic theory, showing how interactions among individuals alter heritable variation in traits, and how this can affect response to selection. The second paper presents general methodology to estimate the quantitative genetic parameters for such traits, and illustrates this methodology using a population of laying hens showing high mortality due to pecking behavior. Neither of those papers report results of a selection experiment.

Because of a ban on the use of beak trimming in some European countries, feather pecking is becoming a substantial problem in the layer industry, both from animal welfare and economic points of view. The feather condition score (FCS) as a measure of feather damage has been shown to be closely related to feather pecking behavior in laying hens housed in groups. To obtain a better understanding of genetic and other biological mechanisms underlying feather pecking behavior, data on FCS of a population of 2,724 female offspring from crossing 50 male W1 and 907 female WB purebred lines were used. The offspring of 25 sires were beak-trimmed, and the offspring of another 25 sires were non-beak-trimmed. Titers of plasma natural antibody (NAb) isotypes IgM and IgG binding keyhole limpet hemocyanin at 24 wk of age were measured. Feather condition was scored at 53 wk of age. In the first part of the present study, we estimated genetic parameters for FCS with 2 variance components models: a traditional linear animal model and a model combining direct and associative genetic effects. In the second part of the present study, a trait-based analysis for FCS was conducted to investigate whether NAb isotype titers can explain variation in FCS among individuals, by fitting a linear mixed model. Though the estimated associative genetic variance was substantial, associative effects for FCS were not statistically significant in both populations (P = 0.09 in beak-trimmed birds, and P = 0.08 in non-beak-trimmed birds). This suggests an insufficient number of records on FCS. Individual's NAb isotypes titers did not show direct effect for FCS of itself, but individual's IgG titers showed a suggestive effect on the FCS of cage mates (associative effect) in beak-trimmed laying hens, which need further confirmation.

International audience; Background Feather pecking is a major welfare issue in laying hen industry that leads to mortality. Due to a ban on conventional cages in the EU and on beak trimming in some countries of the EU, feather pecking will become an even bigger problem. Its severity depends both on the victim receiving pecking and on its group mates inflicting pecking (indirect effects), which together determine plumage condition of the victim. Plumage condition may depend, therefore, on both the direct genetic effect of an individual itself and on the indirect genetic effects of its group mates. Here, we present estimated genetic parameters for direct and indirect effects on plumage condition of different body regions in two purebred layer lines, and estimates of genetic correlations between body regions.MethodsFeather condition scores (FCS) were recorded at 40 weeks of age for neck, back, rump and belly and these four scores were added-up into a total FCS. A classical animal model and a direct–indirect effects model were used to estimate genetic parameters for FCS. In addition, a bivariate model with mortality (0/1) was used to account for mortality before recording FCS. Due to mortality during the first 23 weeks of laying, 5363 (for W1) and 5089 (for WB) FCS records were available.ResultsTotal heritable variance for FCS ranged from 1.5% to 9.8% and from 9.8% to 53.6% when estimated respectively with the classical animal and the direct–indirect effects model. The direct–indirect effects model had a significantly higher likelihood. In both lines, 70% to 94% of the estimated total heritable variation in FCS was due to indirect effects. Using bivariate analysis of FCS and mortality did not affect estimates of genetic parameters. Genetic correlations were high between adjacent regions for FCS on neck, back, and rump but moderate to low for belly with other regions.ConclusionOur results show that 70% to 94% of the heritable variation in FCS relates to indirect effects, indicating that methods of genetic selection that include indirect genetic effects offer perspectives to improve plumage condition in laying hens. This, in turn could reduce a major welfare problem.

Natural antibodies (NAb) are important humoral components of innate immunity. As the first line of defense, NAb provide protection against infection and support adaptive immunity. An earlier study indicated that serum levels of NAb isotypes IgM and IgG at a young age were predictive for survival in non-beak-trimmed purebred laying hens during the laying period. In the present study, genetic parameters of NAb isotypes were estimated and relationships between survival and NAb isotypes levels in crossbred laying hens were investigated. In total, 1,555 beak-trimmed and 1,169 non-beak-trimmed crossbred laying hens were used. Genetic parameters of IgM and IgG titers binding keyhole limpet hemocyanin at 24 wk of age were estimated with a linear animal model. The heritabilities of NAb isotypes IgG and IgM were 0.21 (SE = 0.04) and 0.26 (SE = 0.04), respectively. The genetic correlation between IgG and IgM isotypes was 0.43 (SE = 0.11). These results indicated that NAb isotype titers were heritable traits in the crossbred laying hens. Both NAb isotypes can be selected for simultaneously because the detected positive genetic correlation (0.43, SE = 0.11) between them is positive. Both row and level of the cage were indicated to be associated environmental factors for NAb isotype titers. Different from an earlier study with purebred hens, survival analysis showed no significant associations of survival with NAb isotype titers in beak-trimmed or non-beak-trimmed crossbred hens. Non-health-related causes of mortality, especially in birds with intact beaks, overruled the anticipated relationships between NAb isotype titers and survival.

Background: Through social interactions, individuals affect one another’s phenotype. In such cases, an individual’s phenotype is affected by the direct (genetic) effect of the individual itself and the indirect (genetic) effects of the group mates. Using data on individual phenotypes, direct and indirect genetic (co)variances can be estimated. Together, they compose the total genetic variance that determines a population’s potential to respond to selection. However, it can be difficult or expensive to obtain individual phenotypes. Phenotypes on traits such as egg production and feed intake are, therefore, often collected on group level. In this study, we investigated whether direct, indirect and total genetic variances, and breeding values can be estimated from pooled data (pooled by group). In addition, we determined the optimal group composition, i.e. the optimal number of families represented in a group to minimise the standard error of the estimates. Methods: This study was performed in three steps. First, all research questions were answered by theoretical derivations. Second, a simulation study was conducted to investigate the estimation of variance components and optimal group composition. Third, individual and pooled survival records on 12 944 purebred laying hens were analysed to investigate the estimation of breeding values and response to selection. Results: Through theoretical derivations and simulations, we showed that the total genetic variance can be estimated from pooled data, but the underlying direct and indirect genetic (co)variances cannot. Moreover, we showed that the most accurate estimates are obtained when group members belong to the same family. Additional theoretical derivations and data analyses on survival records showed that the total genetic variance and breeding values can be estimated from pooled data. Moreover, the correlation between the estimated total breeding values obtained from individual and pooled data was surprisingly close to one. This indicates that, for survival in purebred laying hens, loss in response to selection will be small when using pooled instead of individual data. Conclusions: Using pooled data, the total genetic variance and breeding values can be estimated, but the underlying genetic components cannot. The most accurate estimates are obtained when group members belong to the same family.

Through social interactions, individuals can affect one another’s phenotype. The heritable effect of an individual on the phenotype of a conspecific is known as an indirect genetic effect (IGE). Although IGEs can have a substantial impact on heritable variation and response to selection, little is known about the genetic architecture of traits affected by IGEs. We studied IGEs for survival in domestic chickens (Gallus gallus), using data on two purebred lines and their reciprocal cross. Birds were kept in groups of four. Feather pecking and cannibalism caused mortality, as beaks were kept intact. Survival time was shorter in crossbreds than in purebreds, indicating outbreeding depression and the presence of nonadditive genetic effects. IGEs contributed the majority of heritable variation in crossbreds (87 and 72%) and around half of heritable variation in purebreds (65 and 44%). There was no evidence of dominance variance, neither direct nor indirect. Absence of dominance variance in combination with considerable outbreeding depression suggests that survival is affected by many loci. Direct–indirect genetic correlations were moderately to highly negative in crossbreds (−0.37 ± 0.17 and −0.83 ± 0.10), but low and not significantly different from zero in purebreds (0.20 ± 0.21 and −0.28 ± 0.18). Consequently, unlike purebreds, crossbreds would fail to respond positively to mass selection. The direct genetic correlation between both crosses was high (0.95 ± 0.23), whereas the indirect genetic correlation was moderate (0.41 ± 0.26). Thus, for IGEs, it mattered which parental line provided the sire and which provided the dam. This indirect parent-of-origin effect appeared to be paternally transmitted and is probably Z chromosome linked.

Background Mortality due to cannibalism in laying hens is a difficult trait to improve genetically, because censoring is high (animals still alive at the end of the testing period) and it may depend on both the individual itself and the behaviour of its group members, so-called associative effects (social interactions). To analyse survival data, survival analysis can be used. However, it is not possible to include associative effects in the current software for survival analysis. A solution could be to combine survival analysis and a linear animal model including associative effects. This paper presents a two-step approach (2STEP), combining survival analysis and a linear animal model including associative effects (LAM). Methods Data of three purebred White Leghorn layer lines from Institut de Sélection Animale B.V., a Hendrix Genetics company, were used in this study. For the statistical analysis, survival data on 16,780 hens kept in four-bird cages with intact beaks were used. Genetic parameters for direct and associative effects on survival time were estimated using 2STEP. Cross validation was used to compare 2STEP with LAM. LAM was applied directly to estimate genetic parameters for social effects on observed survival days. Results Using 2STEP, total heritable variance, including both direct and associative genetic effects, expressed as the proportion of phenotypic variance, ranged from 32% to 64%. These results were substantially larger than when using LAM. However, cross validation showed that 2STEP gave approximately the same survival curves and rank correlations as LAM. Furthermore, cross validation showed that selection based on both direct and associative genetic effects, using either 2STEP or LAM, gave the best prediction of survival time. Conclusion It can be concluded that 2STEP can be used to estimate genetic parameters for direct and associative effects on survival time in laying hens. Using 2STEP increased the heritable variance in survival time. Cross validation showed that social genetic effects contribute to a large difference in survival days between two extreme groups. Genetic selection targeting both direct and associative effects is expected to reduce mortality due to cannibalism in laying hens.

Social interactions, especially those involving competition among individuals, are important in domesticated livestock and in natural populations. The heritability of traits affected by such interactions has two components, one originating in the individual like that of classical traits (direct effects) and the other originating in other group members (indirect effects). The latter type of trait represents a significant source of ‘hidden heritability’ and it requires population structure and knowledge from relatives in order to access it for selective breeding. When ignored, competitive interactions may increase as an indirect response to direct selection, resulting in diminished yields. We illustrate how population genetic structure affects the response to selection of traits with indirect genetic effects using population genetic and quantitative genetic theory. Population genetic theory permits us to connect our results to the existing body of theory on kin and group selection in natural populations. The quantitative genetic perspective allows us to see how breeders have used knowledge from relatives and family selection in the domestication of plants and animals to improve the welfare and production of livestock by incorporating social genetic effects in the breeding program. We illustrate the central features of these models by reviewing empirical studies from domesticated chickens.

Severe feather pecking is a maladaptive behavior in laying hens that may result in cannibalism and ultimately death of the victims. Selection methods in which the genetic effect of an animal on the survival of its group members is taken into account, i.e. 'group selection', have been shown to be very effective in reducing mortality due to feather pecking and cannibalism in laying hens. It has been suggested that fearfulness and serotonergic functioning are involved in the causation and development of feather pecking. We investigated effects of selection based on survivability in non-beak trimmed groups on fear-related behavior and peripheral 5-HT concentration and uptake in hens with trimmed or intact beaks, in a 2 x 2 factorial arrangement. Hens from the second generation of the low mortality line showed less fear-related behavior than control line hens. In addition, they displayed higher whole blood 5-HT concentrations and a lower platelet 5-HT uptake, indicating differences in functional activity of the 5-HT system. Beak trimming resulted in lowered levels of fear, and in a reduction of feather damage. Hens with trimmed and intact beaks did, however, not differ in peripheral 5-HT. The results imply that fearfulness and 5-HT activity are related to feather pecking without distinguishing between cause and effect. However, given that selection altered fear-related behaviors and peripheral 5-HT concentration and uptake, whereas beak trimming affected fearfulness and feather damage, but not 5-HT parameters, we suggest that peripheral 5-HT activity might reflect the predisposition to develop severe feather pecking under adverse conditions in laying hens.

The aim of the present study was to investigate the effect of brooding and group selection for low mortality on post-stress corticosterone and peripheral serotonin in laying hens. Birds in the experiment originated from the same population and were either group-selected for low mortality (low mortality line) or randomly selected (control line) for two generations. Twelve groups of seven birds from each line were used. Within each line, six groups were brooded by a foster mother and six groups were non-brooded. At 33 weeks of age, birds ( n = 42/treatment) were manually restrained for 5 min, during which their behavioral response (number of struggles) was studied. Fifteen minutes after the start of the manual restraint, blood samples were drawn for assessment of plasma corticosterone and whole blood serotonin (5-HT) concentration. In the low mortality line, 80% of the birds struggled and vocalized vs. 72% in the control line (non significant). Birds from the control line had a higher plasma corticosterone concentration after manual restraint than birds from the low mortality line (7.7 vs. 6.0 nmol ml − 1 ). Furthermore, birds from the control line that were reared without a mother had a lower whole-blood 5-HT concentration than birds from the other treatments (45 vs. 48 nmol ml − 1 ). These results indicate that both brooding and selection for low mortality affect post-stress corticosterone and peripheral serotonin concentration, which may result in a reduced propensity to develop feather pecking.

Livestock populations are usually kept in groups. As a consequence, social interactions among individuals affect productivity, health, and welfare. Current selection methods (individual selection), however, ignore those interactions and yield suboptimal or in some cases even negative responses. In principle, selection between groups instead of individuals offers a solution, but has rarely been adopted in practice for two reasons. First, the relationship between group selection theory and common animal breeding concepts, such as the accuracy of selection, is unclear. Second, application of group selection requires keeping selection candidates in groups, which is often undesirable in practice. This work has two objectives. First, we derive expressions for the accuracy of individual and group selection, which provides a measurement of quality for those methods. Second, we investigate the opportunity to improve traits affected by interactions by using information on relatives kept in family groups, while keeping selection candidates individually. The accuracy of selection based on relatives is shown to be an analogy of the classical expression for traits not affected by interactions. Our results show that selection based on relatives offers good opportunities for effective genetic improvement of traits affected by interactions.

Interactions among individuals are universal, both in animals and in plants and in natural as well as domestic populations. Understanding the consequences of these interactions for the evolution of populations by either natural or artificial selection requires knowledge of the heritable components underlying them. Here we present statistical methodology to estimate the genetic parameters determining response to multilevel selection of traits affected by interactions among individuals in general populations. We apply these methods to obtain estimates of genetic parameters for survival days in a population of layer chickens with high mortality due to pecking behavior. We find that heritable variation is threefold greater than that obtained from classical analyses, meaning that two-thirds of the full heritable variation is hidden to classical analysis due to social interactions. As a consequence, predicted responses to multilevel selection applied to this population are threefold greater than classical predictions. This work, combined with the quantitative genetic theory for response to multilevel selection presented in an accompanying article in this issue, enables the design of selection programs to effectively reduce competitive interactions in livestock and plants and the prediction of the effects of social interactions on evolution in natural populations undergoing multilevel selection.

Impaired claw health is one of the major problems causing production loss and reduced animal welfare in dairy cattle. In response, the Dutch Animal Health Service (GD) Ltd. initiated this study, in which claws of lactating and near-term cows and heifers in 430 herds were trimmed by hoof trimmers and the health status of the rear claws recorded. Only herds with75% of the animals having feet trimmed were considered, resulting in records on 21,611 animals. Eight claw disorders were scored: digital dermatitis (DD), interdigital dermatitis/heel horn erosions (IDHE), sole hemorrhage (SH), chronic laminitis (CL), sole ulcer (SU), white line disease (WLD), interdigital hyperplasia (HYP), and interdigital phlegmona (IP). The prevalence varied from 0.6% (IP) to 39.9% (SH). More than 70% of the animals had at least one claw disorder. Conformation traits and locomotion were recorded once during the animal's first lactation by trained classifiers of the Royal Dutch Cattle Syndicate and completely independent of the moment of claw trimming. Heritabilities were estimated using a sire model, and ranged from0.01 (IP) to 0.10 (DD and HYP). Genetic correlations of incidences of claw disorders with locomotion were variable, ranging from 0.13 (SH) to -0.91 (CL). Genetic correlations with the rear leg conformation traits were lower, ranging from 0.04 (ID with rear leg side view) to -0.69 (IP with rear leg rear view).